Computational Genomics.ppt

Computational Genomics Biology in One Slide: 2 Paradigms High Throughput Biology Biology is becoming an information science Goals of this course Introduction to Computational Biology Basic biology for computer scientists Breadth: mention many topics applications In-depth coverage of Computational Genomics Algorithms for sequence analysis Current applications, trends, and open problems Coverage of useful algorithms Hidden Markov models Dynamic Programming String algorithms Applications of AI techniques Topics in CS262 Part 1: In-depth coverage of basic computational methods for analysis of biological sequences Sequence Alignment Dynamic Programming Hidden Markov models These methods are used heavily in most genomics applications: DNA sequencing Comparison of DNA and proteins across organisms Discovery of genes, promoters, regulatory sites Topics in CS262 Part 2: Topics in computational genomics, more algorithms, and areas of active research DNA sequencing assembly: reading a complete genome such as the human DNA Gene finding: marking genes on the DNA sequence Large-scale comparative genomics: comparing whole genomes from multiple organisms Microarrays regulation: understanding the regulatory code, and potential disease-causing genes RNA structure: predicting the folding of RNA Phylogeny and evolution: quantifying the evolution of biological sequences Course responsibilities Homeworks [72%] 4 challenging problem sets, 4-5 problems/pset Collaboration allowed – please give credit Hws due Thursday, solutions explained Friday Two worst problems in all hws do not count Final [18%] Takehome, 1 day Collaboration not allowed Basic questions – much easier than homeworks Scribing [10%] Due one week after the lecture, except special permission Reading material Books “Biological sequence analysis” by Durbin, Eddy, Krogh, Mitchinson Chapters 1-4, 6, (7-8), (9-10) “Algorithms on strings, trees, and sequences” by Gusfield Chapters (5-7), 11-12, (13),